Is ACTN2 c.126+11del pathogenic?

ACTN2 c.126+11del is classified Benign in ACTN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-11). Absent from gnomAD v4.1; Associated with familial hypertrophic cardiomyopathy.

What condition is associated with ACTN2 c.126+11del?

ACTN2 c.126+11del is associated with familial hypertrophic cardiomyopathy, dilated cardiomyopathy 1AA (ClinVar).

How common is ACTN2 c.126+11del in the general population?

ACTN2 c.126+11del is absent from gnomAD v4.1 (gnomAD).

ACTN2 c.126+11del

rs2102851424 · VCV1600560

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,494,792)

Conditions

familial hypertrophic cardiomyopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +11	near-intronic (+11 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.1	GERP -2.9

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,494,792). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ACTN2
Coding: c.126+11del
MANE Select: NM_001103
dbSNP: rs2102851424
Type: Deletion
Location: chr1:236686807 (GRCh38)
Gene constraint: LOEUF 0.432 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.88 · 18 PDB

Full ACTN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

familial hypertrophic cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1AA

Similar variants

ACTN2 c.242-2_242-1del Uncertain significance ★★ same condition
ACTN2 p.Glu853fs Uncertain significance ★★ same condition
ACTN2 p.Pro240fs Uncertain significance ★★ same condition
ACTN2 p.Leu554fs Likely pathogenic ★ same condition
ACTN2 c.1249_1255+1del Uncertain significance ★ same condition
ACTN2 c.1407-541_1446del Uncertain significance ★ same condition
ACTN2 c.1657-2del Uncertain significance ★ same condition
ACTN2 c.615+4_615+6del Uncertain significance ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/actn2-c-126-plus-11del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown